Brick_load_matrix: Load a NxM dimensional matrix into the Brick store.

In HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

Description

Load a NxM dimensional matrix into the Brick store.

Usage

Brick_load_matrix(
    Brick = NA,
    chr1 = NA,
    chr2 = NA,
    resolution = NA,
    matrix_file = NA,
    delim = " ",
    remove_prior = FALSE,
    num_rows = 2000,
    is_sparse = FALSE,
    sparsity_bins = 100
)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Brick.
chr1	Required. A character vector of length 1 specifying the chromosome corresponding to the rows of the matrix
chr2	Required. A character vector of length 1 specifying the chromosome corresponding to the columns of the matrix
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
matrix_file	Required. A character vector of length 1 specifying the name of the file to load as a matrix into the Brick store.
delim	Optional. Default " " The delimiter of the matrix file.
remove_prior	Optional. Default FALSE If a matrix was loaded before, it will not be replaced. Use remove_prior to override and replace the existing matrix.
num_rows	Optional. Default 2000 Number of rows to read, in each chunk.
is_sparse	Optional. Default FALSE If true, designates the matrix as being a sparse matrix, and computes the sparsity.index. The sparsity index measures the proportion of non-zero rows or columns at a certain distance from the diagonal (100) in cis interaction matrices.
sparsity_bins	Optional. Default 100 With regards to computing the sparsity.index, this parameter decides the number of bins to scan from the diagonal.

Value

Returns TRUE if all went well.

Examples

Bintable.path <- system.file(file.path("extdata", "Bintable_100kb.bins"), 
package = "HiCBricks")

out_dir <- file.path(tempdir(), "matrix_load_test")
dir.create(out_dir)

My_BrickContainer <- Create_many_Bricks(BinTable = Bintable.path, 
    bin_delim = " ", output_directory = out_dir, file_prefix = "Test",
    experiment_name = "Vignette Test", resolution = 100000,
    remove_existing = TRUE)

Matrix_file <- system.file(file.path("extdata", 
"Sexton2012_yaffetanay_CisTrans_100000_corrected_chr2L.txt.gz"), 
package = "HiCBricks")

Brick_load_matrix(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", matrix_file = Matrix_file, delim = " ", 
remove_prior = TRUE, resolution = 100000)

HiCBricks documentation built on Nov. 8, 2020, 7:45 p.m.